3NRJ | pdb_00003nrj

Crystal structure of probable yrbi family phosphatase from pseudomonas syringae pv.phaseolica 1448a complexed with magnesium

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3nrja1	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Pseudomonas savastanoi pv. phaseolicola 1448A ) [TaxId: 264730 ],	SCOPe (2.08)
A	d3nrja2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Pseudomonas savastanoi pv. phaseolicola 1448A ) [TaxId: 264730 ],	SCOPe (2.08)
B	d3nrjb_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Pseudomonas savastanoi pv. phaseolicola 1448A ) [TaxId: 264730 ],	SCOPe (2.08)
C	d3nrjc1	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Pseudomonas savastanoi pv. phaseolicola 1448A ) [TaxId: 264730 ],	SCOPe (2.08)
C	d3nrjc2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Pseudomonas savastanoi pv. phaseolicola 1448A ) [TaxId: 264730 ],	SCOPe (2.08)
D	d3nrjd1	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Pseudomonas savastanoi pv. phaseolicola 1448A ) [TaxId: 264730 ],	SCOPe (2.08)
D	d3nrjd2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Pseudomonas savastanoi pv. phaseolicola 1448A ) [TaxId: 264730 ],	SCOPe (2.08)
E	d3nrje1	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Pseudomonas savastanoi pv. phaseolicola 1448A ) [TaxId: 264730 ],	SCOPe (2.08)
E	d3nrje2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Pseudomonas savastanoi pv. phaseolicola 1448A ) [TaxId: 264730 ],	SCOPe (2.08)
F	d3nrjf1	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Pseudomonas savastanoi pv. phaseolicola 1448A ) [TaxId: 264730 ],	SCOPe (2.08)
F	d3nrjf2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Pseudomonas savastanoi pv. phaseolicola 1448A ) [TaxId: 264730 ],	SCOPe (2.08)
G	d3nrjg1	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Pseudomonas savastanoi pv. phaseolicola 1448A ) [TaxId: 264730 ],	SCOPe (2.08)
G	d3nrjg2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Pseudomonas savastanoi pv. phaseolicola 1448A ) [TaxId: 264730 ],	SCOPe (2.08)
H	d3nrjh1	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Pseudomonas savastanoi pv. phaseolicola 1448A ) [TaxId: 264730 ],	SCOPe (2.08)
H	d3nrjh2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Pseudomonas savastanoi pv. phaseolicola 1448A ) [TaxId: 264730 ],	SCOPe (2.08)
I	d3nrji1	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Pseudomonas savastanoi pv. phaseolicola 1448A ) [TaxId: 264730 ],	SCOPe (2.08)
I	d3nrji2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Pseudomonas savastanoi pv. phaseolicola 1448A ) [TaxId: 264730 ],	SCOPe (2.08)
J	d3nrjj_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Pseudomonas savastanoi pv. phaseolicola 1448A ) [TaxId: 264730 ],	SCOPe (2.08)
K	d3nrjk_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Pseudomonas savastanoi pv. phaseolicola 1448A ) [TaxId: 264730 ],	SCOPe (2.08)
L	d3nrjl_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Pseudomonas savastanoi pv. phaseolicola 1448A ) [TaxId: 264730 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	HAD-like	8081282	3001890	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HAD-like	8081282	3001890	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	HAD-like	8081282	3001890	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	HAD-like	8081282	3001890	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	HAD-like	8081282	3001890	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	HAD-like	8081282	3001890	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	HAD-like	8081282	3001890	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	HAD-like	8081282	3001890	SCOP2B (2022-06-29)
I	SCOP2 Family	Phosphatase YrbI-like	8081281	4003238	SCOP2 (2022-06-29)
I	SCOP2 Superfamily	HAD-like	8081282	3001890	SCOP2 (2022-06-29)
J	SCOP2B Superfamily	HAD-like	8081282	3001890	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	HAD-like	8081282	3001890	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	HAD-like	8081282	3001890	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Hydrolase_3_1	e3nrjA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3_1	ECOD (1.6)
B	Hydrolase_3_1	e3nrjB1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3_1	ECOD (1.6)
C	Hydrolase_3_1	e3nrjC1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3_1	ECOD (1.6)
D	Hydrolase_3_1	e3nrjD1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3_1	ECOD (1.6)
E	Hydrolase_3_1	e3nrjE1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3_1	ECOD (1.6)
F	Hydrolase_3_1	e3nrjF1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3_1	ECOD (1.6)
G	Hydrolase_3_1	e3nrjG1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3_1	ECOD (1.6)
H	Hydrolase_3_1	e3nrjH1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3_1	ECOD (1.6)
I	Hydrolase_3_1	e3nrjI1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3_1	ECOD (1.6)
J	Hydrolase_3_1	e3nrjJ1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3_1	ECOD (1.6)
K	Hydrolase_3_1	e3nrjK1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3_1	ECOD (1.6)
L	Hydrolase_3_1	e3nrjL1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
B	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
C	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
D	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
E	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
F	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
G	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
H	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
I	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
J	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
K	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
L	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	PF08282	haloacid dehalogenase-like hydrolase (Hydrolase_3)	haloacid dehalogenase-like hydrolase	This family contains haloacid dehalogenase-like hydrolase enzymes.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	PROBABLE YRBI FAMILY PHOSPHATASE	phosphoric ester hydrolase activity 3-deoxy-manno-octulosonate-8-phosphatase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity N-acylneuraminate cytidylyltransferase activity cytidylyltransferase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups cation binding ion binding binding phosphoric ester hydrolase activity 3-deoxy-manno-octulosonate-8-phosphatase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity N-acylneuraminate cytidylyltransferase activity cytidylyltransferase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups cation binding ion binding binding metal ion binding small molecule binding	lipopolysaccharide biosynthetic process carbohydrate derivative biosynthetic process carbohydrate metabolic process polysaccharide biosynthetic process carbohydrate biosynthetic process liposaccharide metabolic process lipid biosynthetic process carbohydrate derivative metabolic process primary metabolic process macromolecule biosynthetic process lipopolysaccharide metabolic process polysaccharide metabolic process biosynthetic process metabolic process lipopolysaccharide biosynthetic process carbohydrate derivative biosynthetic process carbohydrate metabolic process polysaccharide biosynthetic process carbohydrate biosynthetic process liposaccharide metabolic process lipid biosynthetic process carbohydrate derivative metabolic process primary metabolic process macromolecule biosynthetic process lipopolysaccharide metabolic process polysaccharide metabolic process biosynthetic process metabolic process cellular process macromolecule metabolic process lipid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR050793	CMP-NeuNAc synthase	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR036412	HAD-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR023214	HAD superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR010023	KdsC family	Family